hgb-bin-proteomics/msannika_exporters

Export MS Annika crosslink results to different formats.

msannika_exporters's Issues

This does not fail if XL position is out of bounds but it SHOULD fail

MSAnnika_exporters/pyXlinkViewerExporter_msannika.py

Line 201 in 657cb32

if seqA[xl_pos_in_alignment] == seqB[xl_pos_in_alignment]:

Windows binary fails to load BLOSUM62 matrix because it is not packaged

MSAnnika_exporters/pyXlinkViewerExporter_msannika.py

Line 77 in fef54fe

Blosum62 = substitution_matrices.load("BLOSUM62")

Proteome Discoverer: Export to pyMOL

Issue is unrelated to currently implemented exporter scripts.

The Proteome Discoverer native "Export to pyMOL" option does not work with MS Annika for some reason (see attached screenshot). Using PyXlinkViewer is preferable in my opinion as it is easier to use without extensive pyMOL knowledge. However, would probably still be a "nice to have" feature at some point to have this working out of the box.

fasta file read error if fasta headers dont contain pipe symbol

Either implement error handling or document that fasta files should follow this standard:

https://www.uniprot.org/help/fasta-headers

Add properly documented manual for usage

Including screenshot and maybe how-to video?

String index out of bounds for PDB structure 7JLT

MSAnnika_exporters/pyXlinkViewerExporter_msannika.py

Line 170 in fef54fe

if seqA[xl_pos_in_alignment] == seqB[xl_pos_in_alignment]:

Export to ChimeraX

ref: hgb-bin-proteomics/MSAnnika#18

Finds first match but match closest to alignment is needed

MSAnnika_exporters/pyXlinkViewerExporter_msannika.py

Line 202 in 657cb32

pep_pos_in_protein = self.sequence.find(seqA)

Argument does not work - change to action = store_false

MSAnnika_exporters/pyXlinkViewerExporter_msannika.py

Line 331 in 657cb32

parser.add_argument("-tp", "--trust_pdb",

Invalid xiVIEW csv exported for ambigous crosslinks

Format seems to be incorrect when exporting ambigous crosslinks to xiVIEW.
Related issue: Rappsilber-Laboratory/build-xiview#94